High-throughput computing

Abstract: SUMMARY Since 1984, the Condor project has enabled ordinary users to do extraordinary computing. Today, the project continues to explore the social and technical problems of cooperative computing on scales ranging from the desktop to the world-wide computational Grid. In this paper, we provide the history and philosophy of the Condor project and describe how it has interacted with other projects and evolved along with the field of distributed computing. We outline the core components of the Condor system and describe how the technology of computing must correspond to social structures. Throughout, we reflect on the lessons of experience and chart the course travelled by research ideas as they grow into production systems. Copyright c � 2005 John Wiley & Sons, Ltd.

Abstract: This paper introduces FireWorks, a workflow software for running high-throughput calculation workflows at supercomputing centers. FireWorks has been used to complete over 50 million CPU-hours worth of computational chemistry and materials science calculations at the National Energy Research Supercomputing Center. It has been designed to serve the demanding high-throughput computing needs of these applications, with extensive support for i concurrent execution through job packing, ii failure detection and correction, iii provenance and reporting for long-running projects, iv automated duplicate detection, and v dynamic workflows i.e., modifying the workflow graph during runtime. We have found that these features are highly relevant to enabling modern data-driven and high-throughput science applications, and we discuss our implementation strategy that rests on Python and NoSQL databases MongoDB. Finally, we present performance data and limitations of our approach along with planned future work. Copyright © 2015 John Wiley & Sons, Ltd.

Abstract: Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules with atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud (EOSC) portal (www.eosc-portal.eu), sending >12 millions of jobs and using around 4000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently.

Abstract: Many-task computing aims to bridge the gap between two computing paradigms, high throughput computing and high performance computing. Many task computing differs from high throughput computing in the emphasis of using large number of computing resources over short periods of time to accomplish many computational tasks (i.e. including both dependent and independent tasks), where primary metrics are measured in seconds (e.g. FLOPS, tasks/sec, MB/s I/O rates), as opposed to operations (e.g. jobs) per month. Many task computing denotes high-performance computations comprising multiple distinct activities, coupled via file system operations. Tasks may be small or large, uniprocessor or multiprocessor, compute-intensive or data-intensive. The set of tasks may be static or dynamic, homogeneous or heterogeneous, loosely coupled or tightly coupled. The aggregate number of tasks, quantity of computing, and volumes of data may be extremely large. Many task computing includes loosely coupled applications that are generally communication-intensive but not naturally expressed using standard message passing interface commonly found in high performance computing, drawing attention to the many computations that are heterogeneous but not ldquohappilyrdquo parallel.